The effect of solvent vapor annealing on the fluorescence properties and morphology of titanyl phthalocyanine/ perylene phenethylimide thin-film molecular semiconductor bilayers (TiOPc/PPEI) is investigated. A combination of atomic force microscopy (AFM) and near-field scanning optical microscopy (NSOM) is used in conjunction with bulk absorption and fluorescence measurements to correlate the morphological and photophysical properties of these bilayer systems. AFM data show that treatment of the vacuum-deposited amorphous PPEI and TiOPc/PPEI films results in the crystalline transformation of these materials and severely alters the contact between the TiOPc and PPEI layers. AFM data show extended solvent vapor annealing produces void spaces in the TiOPc coverage on the order of several hundred nanometers. Steady-state fluorescence intensity and fluorescence lifetime measurements are used as a measure of charge-transfer quenching efficiencies. Very efficient charge-transfer quenching is observed when amorphous layers of TiOPc are deposited onto PPEI resulting from uniform contact between the layers. Extended annealing results in decreased charge-transfer quenching efficiencies as a result of widely dispersed, localized interfacial contact points.